[MMTK] atom connectivity

Michael Sorich mike_sorich@hotmail.com
Mon, 22 Apr 2002 17:04:00 +0930


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Hi, 
 
I have a small molecule (not in the database) which I have loaded from a
pdb file. I am trying to find out what atoms are bonded to an atom. When
I call the bondedTo() function of an atom object, I am returned an empty
list. Am I using the correct function? Is it possible to access
connectivity information for an arbitary molecule with no database
entry? 
 
Thanks
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: michael.sorich@postgrads.unisa.edu.au
           mike_sorich@hotmail.com
 

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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Hi, <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I have a small molecule (not in the database) which I =
have
loaded from a <span class=3DSpellE>pdb</span> file. I am trying to find =
out what atoms
are bonded to an atom. When I call the <span class=3DSpellE><span =
class=3DGramE>bondedTo</span></span><span
class=3DGramE>(</span>) function of an atom object, I am returned an =
empty list. Am
I using the correct function? Is it possible to access connectivity =
information
for an <span class=3DSpellE>arbitary</span> molecule with no database =
entry? <o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thanks<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Michael =
Sorich<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>PhD =
Student<o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place><st1:PlaceType><font size=3D2 =
face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>School</spa=
n></font></st1:PlaceType><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
 yes'> of </span></font><st1:PlaceName><font size=3D2 face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>Pharmaceuti=
cal</span></font></st1:PlaceName></st1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'>, Molecular and Biomedical Sciences<o:p></o:p></span></font></p>

<p class=3DMsoNormal><st1:place><st1:PlaceType><font size=3D2 =
face=3DArial><span
  =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>University<=
/span></font></st1:PlaceType><font
 size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
 yes'> of </span></font><st1:PlaceName><font size=3D2 face=3DArial><span
  style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:yes'>South =
Australia</span></font></st1:PlaceName></st1:place><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial;mso-no-proof:
yes'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'>Email:
michael.sorich@postgrads.unisa.edu.au<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial;mso-no-proof:yes'><span
style=3D'mso-spacerun:yes'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;
</span>mike_sorich@hotmail.com<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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